Variant report

Variant	rs11603330
Chromosome Location	chr11:71153459-71153460
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:71151944-71156747	K562	blood:	n/a	n/a
2	POLR2A	chr11:71153283-71153509	K562	blood:	n/a	n/a
3	POLR2A	chr11:71153241-71154120	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:71146059..71148297-chr11:71153188..71155860,2	K562	blood:
2	chr11:71150692..71153685-chr11:71157371..71159231,2	K562	blood:

Variant related genes	Relation type
DHCR7	TF binding region
ENSG00000172893	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1044482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11233746	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11233747	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11233789	0.85[EUR][1000 genomes]
rs11546509	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11600569	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11600860	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11604642	0.84[ASN][1000 genomes]
rs11606033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11606612	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11606631	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12278461	0.85[EUR][1000 genomes]
rs12419279	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12419334	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12422045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12785878	0.95[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12789253	0.81[ASN][1000 genomes]
rs12789751	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12790010	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12790558	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12791871	0.95[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12792306	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12793224	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12793530	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12793607	0.81[ASN][1000 genomes]
rs12794668	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12797951	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12800438	0.95[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12803256	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12806844	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12806918	0.91[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap]
rs12807718	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12807827	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12808368	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1630498	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs1790324	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs1790345	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs1792229	0.81[TSI][hapmap]
rs1792277	0.81[CEU][hapmap]
rs1792282	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs1792284	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs1981412	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2002063	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2002064	0.81[TSI][hapmap]
rs2040323	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2276360	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2276361	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2276362	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2282620	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2282621	0.95[CEU][hapmap];0.80[CHD][hapmap];0.96[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs28364617	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2852853	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3750997	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3763856	0.81[ASN][1000 genomes]
rs3794060	0.95[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4423214	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4488226	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4944044	0.87[CHB][hapmap]
rs4944062	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4944946	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944949	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4944955	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4944956	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4944957	0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs4944958	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4944959	0.95[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4944996	0.92[ASN][1000 genomes]
rs4945008	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs732934	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs736894	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs7928249	0.95[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7935125	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7938885	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7944926	0.95[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs909217	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv526973	chr11:71088949-71215880	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv897897	chr11:71088949-71217571	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
5	nsv897898	chr11:71103143-71211654	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv519224	chr11:71108341-71215880	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
7	nsv518163	chr11:71142350-71155153	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11603330	NADSYN1	cis	Nerve Tibial	GTEx
rs11603330	FOLR3	cis	parietal	SCAN
rs11603330	RAB6A	cis	cerebellum	SCAN
rs11603330	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs11603330	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11603330	NADSYN1	cis	Thyroid	GTEx
rs11603330	RP11-660L16.2	cis	Heart Left Ventricle	GTEx
rs11603330	RP11-660L16.2	cis	Whole Blood	GTEx
rs11603330	DHCR7	cis	cerebellum	SCAN
rs11603330	RP11-660L16.2	cis	Esophagus Muscularis	GTEx
rs11603330	RP11-660L16.2	cis	Adipose Subcutaneous	GTEx
rs11603330	RP11-660L16.2	cis	Thyroid	GTEx
rs11603330	NADSYN1	cis	lung	GTEx
rs11603330	RP11-660L16.2	cis	Nerve Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71140600-71158200	Weak transcription	Fetal Brain Male	brain
2	chr11:71140800-71154000	Weak transcription	Fetal Lung	lung
3	chr11:71140800-71154000	Weak transcription	HSMM	muscle
4	chr11:71144000-71156200	Strong transcription	Fetal Brain Female	brain
5	chr11:71144200-71158200	Weak transcription	Small Intestine	intestine
6	chr11:71144400-71156200	Strong transcription	Primary T cells from cord blood	blood
7	chr11:71144600-71157800	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr11:71144800-71156600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:71144800-71156800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:71144800-71156800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr11:71144800-71157800	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr11:71145000-71155400	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr11:71145000-71156400	Strong transcription	Brain Germinal Matrix	brain
14	chr11:71145000-71156600	Strong transcription	Fetal Stomach	stomach
15	chr11:71145000-71157000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr11:71145000-71157000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:71145000-71157400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:71145000-71157800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:71145000-71158600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr11:71145200-71156200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr11:71145200-71157000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr11:71145200-71157000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr11:71145200-71157200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr11:71145200-71157400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr11:71145200-71157400	Strong transcription	HMEC	breast
26	chr11:71145200-71157800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr11:71145400-71157800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr11:71145400-71158000	Weak transcription	Stomach Mucosa	stomach
29	chr11:71145600-71157000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr11:71145600-71157000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr11:71145600-71158000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr11:71145800-71155400	Strong transcription	Left Ventricle	heart
33	chr11:71145800-71156200	Strong transcription	Lung	lung
34	chr11:71145800-71156400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:71145800-71156600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:71145800-71156600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr11:71145800-71156800	Strong transcription	Duodenum Mucosa	Duodenum
38	chr11:71145800-71156800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr11:71145800-71157000	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr11:71145800-71157200	Strong transcription	HSMMtube	muscle
41	chr11:71145800-71157400	Strong transcription	Fetal Intestine Large	intestine
42	chr11:71145800-71157800	Strong transcription	Fetal Intestine Small	intestine
43	chr11:71146000-71153800	Strong transcription	Brain Cingulate Gyrus	brain
44	chr11:71146000-71155800	Strong transcription	HepG2	liver
45	chr11:71146000-71156200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr11:71146000-71156800	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr11:71146000-71156800	Strong transcription	Fetal Muscle Leg	muscle
48	chr11:71146000-71157000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr11:71146000-71157000	Strong transcription	Dnd41	blood
50	chr11:71146000-71158000	Strong transcription	HUES48 Cell Line	embryonic stem cell

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